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Kurisu, Genji; Kusunoki, Masami; Katoh, Etsuko; Yamazaki, Toshimasa; Teshima, Keizo; Onda, Yayoi; Kimata‐Ariga, Yoko; Hase, Toshiharu

doi:10.1038/84097

Cited by 308 publications

(180 citation statements)

References 30 publications

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“…The B factors in the NADP ϩ -flexible subdomain in the two conformers differ considerably (Fig. 4D) (16), and this motional difference in crystals is consistent with the difference in our PF profiles in solution at pD r 8.0 and 6.0. In addition, most of the residues of FNR that were largely perturbed in their chemical shifts upon binding of NADP ϩ at pH 8.0 existed in the NADP ϩ -flexible subdomain, suggesting that the motional mode is important for the substrate binding (Fig.…”

Section: Discussionsupporting

confidence: 72%

“…In contrast, loop regions between ␣-helices and ␤ strands and N-and C-terminal regions were least protected from exchange. FNR has a characteristic N-terminal region composed of 30 amino acid residues that form unstructured conformation as indicated by x-ray (16) and NMR analyses (20). The results of H/D exchange showing no protected residue in this region were consistent with the x-ray structure, confirming the flexibility in the N-terminal region.…”

Section: Global Unfolding Of Fnr Induced By Urea-wesupporting

confidence: 72%

“…The activity and affinities for substrates of FNR decreased in response to a pH change from about 8 to 6 in chloroplasts (15). The three-dimensional structure of maize FNR composed of the well defined FAD-and NADP ϩ -binding domains has been solved by x-ray crystallography (16). The FAD-binding domain (residues 1 to 153) is made up of a sixstranded antiparallel ␤-barrel the bottom of which is capped by an ␣-helix and a long loop.…”

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confidence: 99%

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Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

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NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residuebased conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP ؉ reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP ؉ )-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD r values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD r values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP ؉ -binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP ؉ -binding domain at pD r 8.0, the daytime pH in chloroplasts, than at pD r 6.0 is likely to be involved in the increased binding of NADP ؉ for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.Protein conformations as shown by x-ray crystallography or nuclear magnetic resonance spectroscopy are virtually dynamic entities over various time ranges in solution (1, 2). Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3-5). The hydrogen/deuterium (H/D) 4 exchange of amide protons in backbones has become an important way to address the motions of a protein from small or relatively large scale motions involved in biological functions such as binding of a substrate or releasing a product to much more large scale motions like a global unfolding process (4, 6). Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7). For many globular proteins, this approach has identified protected cores, which are often composed of secondary structures buried inside the molecules and the cooperative interactions with partner molecules (4, 8), leading to allostery (9). Detailed analyses of exchanges in the native state of cytochrome c in the presence of various concentrations of denaturants suggested a pathway to unfolding, in which groups of secondary structural elements (i.e. foldons) are unfolded sequentially through distin...

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Section: Discussionsupporting

confidence: 72%

Section: Global Unfolding Of Fnr Induced By Urea-wesupporting

confidence: 72%

mentioning

confidence: 99%

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Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

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“…There is precedence for such variable interdomain contacts among FNR family proteins. For instance, in the maize leaf ferredoxin (Fd)-FNR complex, the Fd protein is rotated ϳ180°about the [2Fe-2S]-flavin axis with respect to the PDR domain arrangement (40). Aligning the FAD/NADH domains of PDR with those of benzoate 1,2-dioxygenase reductase from Acinetobacter sp.…”

Section: Domain Engineering Of the Smmo Reductase 5637mentioning

confidence: 99%

Domain Engineering of the Reductase Component of Soluble Methane Monooxygenase from Methylococcus capsulatus (Bath)

Blazyk

Lippard

2004

Journal of Biological Chemistry

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The first step in the catabolic pathway of methanotrophs is the conversion of methane to methanol by soluble or membrane-bound methane monooxygenases (MMOs) 1 (1, 2). Although the soluble MMO (sMMO) system is expressed by only a few organisms under low copper conditions (3), it has been characterized far more extensively than the particulate form because of difficulties purifying and stabilizing the particulate MMO enzymes (4 -6). The sMMO proteins from two methanotrophic bacteria, Methylococcus capsulatus (Bath) (7,8) and Methylosinus trichosporium OB3b (9, 10), have been studied in great detail (11)(12)(13)(14)(15)(16)(17)(18)(19). Both systems require three components: a dimeric (␣␤␥) 2 hydroxylase (MMOH, 251 kDa) with dinuclear, carboxylate-bridged iron centers, where dioxygen activation and methane hydroxylation occur; a regulatory protein (MMOB, 15.9 kDa); and a reductase (MMOR, 38.5 kDa) that transfers electrons from NADH to the MMOH diiron sites, thereby priming the hydroxylase for reaction with dioxygen. The N-terminal domain of MMOR, which houses a [2Fe-2S] cluster, shares sequence (20), spectroscopic (16,(21)(22)(23)(24), and structural (25) properties with ferredoxins of plants, cyanobacteria, and archaebacteria. A flavin adenine dinucleotide (FAD) cofactor located in the C-terminal portion of MMOR accepts two electrons from NADH. These electrons are passed sequentially from the reduced FAD moiety through the MMOR [2Fe-2S] center into the hydroxylase active sites by means of a series of intra-and intermolecular electron transfer reactions (16,24,26,27).MMOR is a member of a class of modular flavoprotein electron transferases, also known as the ferredoxin:NADP ϩ oxidoreductase (FNR) family. These proteins contain a flavin domain that transfers electrons between a nicotinamide dinucleotide and a one-electron carrier domain, which may be linked or dissociable (28 -30). Because the electron carrier domain can be attached to either the N-or C-terminal end of the core flavin/NAD(P) unit, this domain appears to be an independent modular element. In support of this designation, the crystal structure of Burkholderia cepacia phthalate dioxygenase reductase (PDR), an FNR family member with C-terminal electron carrier connectivity, shows distinct flavin mononucleotide (FMN), NADH binding, and [2Fe-2S] domains ( Fig. 1) (30). To examine the modular nature of MMOR and facilitate characterization of this complex protein, the ferredoxin (MMOR-Fd) and FAD/NADH (MMOR-FAD) domains were expressed as separate polypeptides (31). NMR studies reveal that * This work was supported by National Institutes of Health Research Grant GM32134 (to S. J. L.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.‡ Howard Hughes Medical Institute predoctoral fellow. § To whom correspondence should be addressed.

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“…The crystal structure of maize Fd isoform I (FdI) in complex with FNR revealed for the first time that binding of Fd induces conformational changes in the active site of FNR which may be involved in modulation of its enzymatic activity (Kurisu et al, 2001). Furthermore, the X-ray structure of Equisetum arvense ferredoxin isoform II (FdII) provided evidence for putative differences in the binding modes of FdI and FdII to FNR (Kurisu et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase fromLeptospira interrogans

et al. 2006

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Ferredoxin-NADP + reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 Å resolution at a synchrotron source.

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Untitled

Cited by 308 publications

References 30 publications

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Domain Engineering of the Reductase Component of Soluble Methane Monooxygenase from Methylococcus capsulatus (Bath)

Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase fromLeptospira interrogans

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